Students at the Al-Fatah Pesantren, during Eid al-Fitr celebrations, August 12, 2015.

A Muslim academy for transgender women that made headlines in the U.S. and Europe since opening in 2008 was closed on Thursday by officials in Indonesia's Yogyakarta region following protests by an organization calling itself the Islamic Jihad Front.

The head of the local jurisdiction home to the school, known as the Al Fatah Pesantren, confirmed its closure to BuzzFeed News on Friday. It is the latest development in an uproar over LGBT rights that began in January, which has caught the country's LGBT activists by surprise. Until last month, anti-LGBT rhetoric was not a major feature of politics in Indonesia, which is home to more Muslims than any nation in the world. The country has long been home to a community of transgender women known as waria, and the school — which has about 40 students — has received so much attention in the Western press in part because it symbolized pluralism and strands of progressive Islam that distinguished Indonesia's religious life.

The storm over LGBT issues began in January when the minister with oversight of higher education pronounced LGBT student groups to be incompatible with “standards of values and morals” expected at the country's universities.

Though some political leaders appear to have tried to quiet the uproar, others are eagerly pouring flames on the fire. On Monday, Defense Minister Ryamizard Ryacudu suggested the LGBT community is more dangerous than nuclear weapons, because "it skews the mindset of our nation away from our base ideology." On Friday, former Information and Communications Minister Tifatul Sembering, who now is an MP from the Islamist Prosperous Justice Party, tweeted, “A saying of the Prophet [Mohamed]: Whomever you find committing the acts of the community of Lot (homosexual) should be put to death," though he later deleted the tweet.

Until this year, the Al Fatah Pesantren operated without major problems, according to the school's director, Shinta Ratri, who spoke to BuzzFeed News by phone this week. In fact, she said, the country's waria community wasn't even perceived as connected to gays and lesbians nor the activists with ties to international LGBT organizations.

"Before people still understood that waria is separate from LGBT, but now even us waria have been becoming part of the LGBT," she said.

They had never had trouble with the Islamic Jihad Front, an organization founded around the same time as the school that claims 150 members. The organization's purpose is to "improve the public's understanding of Islam" and tackle “social disease,” said a man known as Darohman in Indonesian and Abu Dzaki in Arabic in a phone interview with BuzzFeed News. He is the leader of the group's "militia" which also has taken action to shut down a karaoke bar, harass Shiite muslims, and close a Christian church supposedly operating without a proper license, according to the group's website.

Last Friday morning, Darrohman told Buzzfeed News, the group broadcast a text message to its members that read, "We invite all Muslim Brothers to REFUSE and SHUTTER" the school. It was called an "Invitation to uphold what is right and rejecting what is wrong."

Darrohman told BuzzFeed News the group moved on the waria school because they'd heard the group was working on drafting fiqih — codes on religious obligations — for transgender women, and wanted "an official explanation."

The school's organizer's had heard about the text message before a group of 20 FJI members showed up, and the students of the school had fled to an office of a legal aid organization, Shinta said, and the local police responded to protect the school.

"We will provide security without any time limit; this is my territory," the local police commander, Suharno, said to CNN Indonesia. "We will also deploy [officers] to watch every day, every second to do security."

But on Thursday, a local official announced that they would close the school and ban religious activities on the grounds citing concerns about "public order," the Jakarta Post reported.

The head of the local government, Jati Bayubroto of the Bangun Papan subdistrict of Bantul, Yogyakarta, told BuzzFeed News by phone that the school was also facing complaints from neighbors over issues like noise and congestion when they held events. It meant in a house belonging to Shinta's relative and the neighbors said it also hosted karaoke and served alcohol. But, he said, the neighbors were also afraid that they would be targeted by groups like the FJI.

"For almost two years, people have been tolerant to the activities at the house of Ibu Shinta’s relative," he said. "But when the situation is threatening security, they are afraid something could happen in the neighborhood. They demand the closure of the place. In addition, they are also afraid that their activities could negatively affect the local kids."

The decision to close the school followed a meeting organized by local officials between the FJI and the school's organizers, which a lawyer for the school told the Jakarta Post was rigged against the school.

"The FJI's pressure is not a legal regulation that must be followed," the lawyer, Aditia Arief Firmanto, told the paper.

Shinta declined to speak to reporters after the meeting, telling the Jakarta Post by text message, "I am psychologically tired."

But she vowed she would continue fighting to provide religious instruction to her students when she spoke to BuzzFeed News earlier in the week.

"I will not give up to provide facility to our friends in the waria community to worship, to practice the Islamic way," she said.

J. Lester Feder is a world correspondent for BuzzFeed News and is based in Washington, DC. His secure PGP fingerprint is 2353 DB68 8AA6 92BD 67B8 94DF 37D8 0A6F D70B 7211